Exclusion Processes with Internal States

We introduce driven exclusion processes with internal states that serve as generic transport models in various contexts, ranging from molecular or vehicular traffic on parallel lanes to spintronics. The ensuing non-equilibrium steady states are controllable by boundary as well as bulk rates. A striking polarization phenomenon accompanied by domain wall motion and delocalization is discovered within a mesoscopic scaling. We quantify this observation within an analytic description providing exact phase diagrams. Our results are confirmed by stochastic simulations.Comment: 4 pages, 3 figures. Version as published in Phys. Rev. Let

Generic principles of active transport

Nonequilibrium collective motion is ubiquitous in nature and often results in a rich collection of intringuing phenomena, such as the formation of shocks or patterns, subdiffusive kinetics, traffic jams, and nonequilibrium phase transitions. These stochastic many-body features characterize transport processes in biology, soft condensed matter and, possibly, also in nanoscience. Inspired by these applications, a wide class of lattice-gas models has recently been considered. Building on the celebrated {\it totally asymmetric simple exclusion process} (TASEP) and a generalization accounting for the exchanges with a reservoir, we discuss the qualitative and quantitative nonequilibrium properties of these model systems. We specifically analyze the case of a dimeric lattice gas, the transport in the presence of pointwise disorder and along coupled tracks.Comment: 21 pages, 10 figures. Pedagogical paper based on a lecture delivered at the conference on "Stochastic models in biological sciences" (May 29 - June 2, 2006 in Warsaw). For the Banach Center Publication

Domain wall delocalization, dynamics and fluctuations in an exclusion process with two internal states

We investigate the delocalization transition appearing in an exclusion process with two internal states resp. on two parallel lanes. At the transition, delocalized domain walls form in the density profiles of both internal states, in agreement with a mean-field approach. Remarkably, the topology of the system's phase diagram allows for the delocalization of a (localized) domain wall when approaching the transition. We quantify the domain wall's delocalization close to the transition by analytic results obtained within the framework of the domain wall picture. Power-law dependences of the domain wall width on the distance to the delocalization transition as well as on the system size are uncovered, they agree with numerical results.Comment: 10 pages, 5 figure

Comparison of the Effects of Early Pregnancy with Human Interferon, Alpha 2 (IFNA2), on Gene Expression in Bovine Endometrium

Interferon tau (IFNT), a type I IFN similar to alpha IFNs (IFNA), is the pregnancy recognition signal produced by the ruminant conceptus. To elucidate specific effects of bovine IFNT and of other conceptus-derived factors, endometrial gene expression changes during early pregnancy were compared to gene expression changes after intrauterine application of human IFNA2. In experiment 1, endometrial tissue samples were obtained on Day (D) 12, D15, and D18 postmating from nonpregnant or pregnant heifers. In experiment 2, heifers were treated from D14 to D16 of the estrous cycle with an intrauterine device releasing IFNA2 or, as controls, placebo lipid extrudates or PBS only. Endometrial biopsies were performed after flushing the uterus. All samples from both experiments were analyzed with an Affymetrix Bovine Genome Array. Experiment 1 revealed differential gene expression between pregnant and nonpregnant endometria on D15 and D18. In experiment 2, IFNA2 treatment resulted in differential gene expression in the bovine endometrium. Comparison of the data sets from both studies identified genes that were differentially expressed in response to IFNA2 but not in response to pregnancy on D15 or D18. In addition, genes were found that were differentially expressed during pregnancy but not after IFNA2 treatment. In experiment 3, spatiotemporal alterations in expression of selected genes were determined in uteri from nonpregnant and early pregnant heifers using in situ hybridization. The overall findings of this study suggest differential effects of bovine IFNT compared to human IFNA2 and that some pregnancy-specific changes in the endometrium are elicited by conceptus-derived factors other than IFNT

Driven transport on parallel lanes with particle exclusion and obstruction

We investigate a driven two-channel system where particles on different lanes mutually obstruct each other's motion, extending an earlier model by Popkov and Peschel Phys. Rev. E 64, 026126 (2001)]. This obstruction may occur in biological contexts due to steric hinderance where motor proteins carry cargos by "walking" on microtubules. Similarly, the model serves as a description for classical spin transport where charged particles with internal states move unidirectionally on a lattice. Three regimes of qualitatively different behavior are identified, depending on the strength of coupling between the lanes. For small and large coupling strengths the model can be mapped to a one-channel problem, whereas a rich phase behavior emerges for intermediate ones. We derive an approximate but quantitatively accurate theoretical description in terms of a one-site cluster approximation, and obtain insight into the phase behavior through the current-density relations combined with an extremal-current principle. Our results are confirmed by stochastic simulations

Traffic jams induced by rare switching events in two-lane transport

We investigate a model for driven exclusion processes where internal states are assigned to the particles. The latter account for diverse situations, ranging from spin states in spintronics to parallel lanes in intracellular or vehicular traffic. Introducing a coupling between the internal states by allowing particles to switch from one to another induces an intriguing polarization phenomenon. In a mesoscopic scaling, a rich stationary regime for the density profiles is discovered, with localized domain walls in the density profile of one of the internal states being feasible. We derive the shape of the density profiles as well as resulting phase diagrams analytically by a mean-field approximation and a continuum limit. Continuous as well as discontinuous lines of phase transition emerge, their intersections induce multi-critical behaviour

An All-Atom Force Field for Dry and Water-Lubricated Carbon Tribological Interfaces

We present a non-reactive force field for molecular dynamics simulations of interfaces between passivated amorphous surfaces and their interaction with water. The force field enables large-scale dynamic simulations of dry and lubricated tribological contacts and is tailored to surfaces with hydrogen, hydroxyl and aromatic surface passivation. To favour its compatibility with existing force-field parameterizations for liquids and allow a straightforward extension to other types of surface passivation species, we adopt the commonly used OPLS functional form. The optimisation of the force-field parameters is systematic and follows a protocol that can be reused for other surface-molecule combinations. Reference data are calculated with gradient- and dispersion-corrected density functional theory and include the bonding structure and elastic deformation of bulk and surface structures as well as surface adhesion and water adsorption energy landscapes. The conventions adopted to define the different force-field atom types are based on the hybridisation of carbon orbitals and enable a simple and efficient parameter optimisation strategy based on quantum-mechanical calculations performed only on crystalline reference structures. Transferability tests on amorphous interfaces demonstrate the effectiveness of this approach. After testing the force field, we present two examples of application to tribological problems. Namely, we investigate relationships between dry friction and the corrugation of the contact potential energy surface and the dependency of friction on the thickness of interface water films. We finally discuss the limitations of the force field and propose strategies for its improvement and extension

Involvement of A1 adenosine receptors in osmotic volume regulation of retinal glial cells in mice

PURPOSE: Osmotic swelling of Müller glial cells has been suggested to contribute to retinal edema. We determined the role of adenosine signaling in the inhibition of Müller cell swelling in the murine retina. METHODS: The size of Müller cell somata was recorded before and during perfusion of retinal sections and isolated Müller cells with a hypoosmolar solution. Retinal tissues were freshly isolated from wild-type mice and mice deficient in A(1) adenosine receptors (A(1)AR(-/-)), or cultured as whole-mounts for three days. The potassium conductance of Müller cells was recorded in isolated cells, and retinal slices were immunostained against Kir4.1. RESULTS: Hypotonic exposure for 4 min induced a swelling of Müller cell bodies in retinal slices from A(1)AR(-/-) mice but not wild-type mice. Pharmacological inhibition of A(1) receptors or of the ecto-5'-nucleotidase induced hypoosmotic swelling of Müller cells from wild-type mice. Exogenous adenosine prevented the swelling of Müller cells from wild-type but not A(1)AR(-/-) mice. The antiinflammatory corticosteroid, triamcinolone acetonide, inhibited the swelling of Müller cells from wild-type mice; this effect was blocked by an antagonist of A(1) receptors. The potassium conductance of Müller cells and the Kir4.1 immunolabeling of retinal slices were not different between A(1)AR(-/-) and wild-type mice, both in freshly isolated tissues and retinal organ cultures. CONCLUSIONS: The data suggest that autocrine activation of A(1) receptors by extracellularly generated adenosine mediates the volume homeostasis of Müller cells in the murine retina. The swelling-inhibitory effect of triamcinolone is mediated by enhancement of endogenous adenosine signaling

magnetoARPES: Angle Resolved Photoemission Spectroscopy with Magnetic Field Control

Angle-Resolved Photoemission Spectroscopy (ARPES) is a premier technique for understanding the electronic excitations in conductive, crystalline matter, in which the induced photocurrent is collected and dispersed in energy and angle of emission to reveal the energy- and momentum-dependent single particle spectral function $A(\mathbf{k},\omega)$. So far, ARPES in a magnetic field has been precluded due to the need to preserve the electron paths between the sample and detector. In this paper we report progress towards "magnetoARPES", a variant of ARPES that can be conducted in a magnetic field. It is achieved by applying a microscopic probe beam ($\lesssim$ 10 $\mu$m ) to a thinned sample mounted upon a special sample holder that generates magnetic field confined to a thin layer near the sample surface. In this geometry we could produce ARPES in magnetic fields up to around $\pm$ 100 mT. The magnetic fields can be varied from purely in-plane to nearly purely out-of-plane, by scanning the probe beam across different parts of the device. We present experimental and simulated data for graphene to explore the aberrations induced by the magnetic field. These results demonstrate the viability of the magnetoARPES technique for exploring symmetry breaking effects in weak magnetic fields.Comment: 21 pages, 6 figure